Elite controllers as a model for a cure of HIV-1 infection

摘要 虽然有报道称，在两个人的干细胞移植后，HIV-1感染的无菌治愈。 CCR5HIV-1 32纯合子细胞，∆-1的自发功能治愈在所有感染的人中发生在0.3%-0.5% 个人。这些人被称为精英管制员(EC)，他们保持着无法检测到的艾滋病毒1复制水平 尽管反复从病毒库细胞中分离出具有复制能力的病毒，但缺乏治疗。 这些人提供了活生生的证据，表明自发控制HIV-1感染是可能的，而且 确定这种显著疾病结果背后的病毒学和免疫学机制是成立的 有望在更广泛的HIV-1患者群体中诱导HIV-1感染的功能性治愈。在这里，我们建议 EC中未检测到的病毒载量与特定的遗传和表观遗传特征有关的新假说 储存细胞中的前病毒HIV-1 DNA。基于强有力的初步数据，我们假设完整的HIV-1病毒 来自EC的病毒优先位于不允许有效病毒基因的非基因染色体区域 转录，导致潜伏期很长的前病毒环境，对 活体内的再激活刺激。此外，我们提出，来自EC的完整前病毒也经常被整合 进入显示抑制染色质表观遗传特征的染色体区域，证据是增强的 与可及染色质的距离，以及富含抑制性组蛋白标记和高甲基化DNA。至 为此，我们计划纵向分析完整前病毒的频率和染色体位置。 在EC的血液和淋巴组织中，使用新的实验和生物计算分析方法 (具体目标1)。此外，我们将对表观遗传的染色质特征进行详细的分析 完整前病毒的整合位点，使用下一代测序分析进行全基因组表征 染色质可及性、RNA转录、激活和抑制组蛋白标记以及DNA甲基化 (具体目标2)。最后，我们将进行功能性实验来评估对病毒重新激活的反应性 刺激，使用新的单细胞分析同时表征前病毒序列，染色体 单个病毒库细胞的整合位点和HIV-1转录活性(特异靶3)；这些高度 创新的单库细胞分析将允许对染色体位置的假设进行功能性测试 EC中完整的前病毒维持着一种深潜伏期状态，并对病毒重新激活刺激具有抵抗力。如果 这个项目的成功将极大地扩展我们目前对自然、无药物控制的理解 在更广泛的患者群体中诱导自然控制是可能的，并具有很高的信息量。

Abstract While a sterilizing cure of HIV-1 infection has been reported in two individuals after a stem cell transplant with CCR5∆32 homozygous cells, a spontaneous functional cure of HIV-1 occurs in 0.3-0.5% of all infected individuals. These individuals, termed elite controllers (EC), maintain undetectable levels of HIV-1 replication in the absence of treatment, despite the repeated isolation of replication-competent virus from viral reservoir cells. These individuals provide living evidence that spontaneous control of HIV-1 infection is possible, and the identification of virological and immunological mechanisms underlying such a remarkable disease outcome holds promise for inducing a functional cure of HIV-1 infection in broader HIV-1 patient populations. Here, we propose the novel hypothesis that undetectable viral loads in EC are related to specific genetic and epigenetic features of proviral HIV-1 DNA in reservoir cells. Based on strong preliminary data, we posit that intact HIV-1 proviruses from EC are preferentially located in non-genic chromosomal regions that do not permit effective viral gene transcription, resulting in a proviral landscape in deep latency and with very limited responsiveness to reactivation stimuli in vivo. In addition, we propose that intact proviruses from EC are also frequently integrated into chromosomal regions that show epigenetic characteristics of repressive chromatin, evidenced by enhanced distance to accessible chromatin and enrichment with inhibitory histone marks and hypermethylated DNA. To investigate this, we plan to longitudinally analyze the frequency and chromosomal location of intact proviruses in blood and lymphoid tissues of EC, using novel experimental and biocomputational analysis approaches (Specific Aim 1). In addition, we will conduct a detailed analysis of epigenetic chromatin features at the integration sites of intact proviruses, using next-generation sequencing assays for genome-wide characterization of chromatin accessibility, RNA transcription, activating and inhibitory histone marks, and DNA methylation (Specific Aim 2). Finally, we will perform functional experiments to evaluate responsiveness to viral reactivation stimuli, using novel single-cell assays to simultaneously characterize proviral sequence, chromosomal integration sites and HIV-1 transcriptional activity of single viral reservoir cells (Specific Aim 3); these highly innovate single-reservoir-cell assays will allow to functionally test the hypothesis that chromosomal locations of intact proviruses in EC maintain a state of deep latency and confer resistance to viral reactivation stimuli. If successful, this project will significantly expand our current understanding of how natural, drug-free control is possible, and be highly informative for inducing natural control in broader patient populations.